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CMS vs purely Custom, for complex website

I would like to get others' opinion on whether or not to use Joomla for a project that I and a team are starting. I have no experience with Joomla, and have always developed my projects purely in my own PHP code. To me this seems like the best way forward for our new project as well, but one of our top developers believes fully in using Joomla.

The project involves a fairly complex website, with lots of functionality -- two types of user accounts, administrator accounts/panel to manage/monitor users, transactions between users (eg purchases), and use of third-party APIs (one of our own + Facebook sign-in, etc). I typically think of a CMS as being used for blog/article/content sites, but I understand that any needed functionality could be coded into extensions/plugins/modules/components.

The website will be responsive and adapt to mobile screens.

There will also be native mobile apps. The core functionality of everything will be written as PHP web services, which both the website and app will tap into.

If I had to give an example of what the project is similar to I'd have to say it's akin to the Google Play Store / etc, where you have developers, users, media being searched/browsed/purchased, and all of the related account functions for those two types of users.

We would like people on our team who aren't familiar with coding to be able to make some content changes to the site. Although any changes would ideally be commitable to our subversion repository.

I worry about a few things:
- ability to maintain local/subversion copies of everything, when content changes are made via the Joomla template editing system
- spreading both our PHP and HTML code into lots of modules/templates/etc, making it confusing to edit
- variable scope for when different website elements need to share variables/data
- security/bugs and having to apply patches which may break something
- whether we truly have as much flexibility as a custom-coded project. And if we have to step outside the extensions and edit actual joomla files for any reason then applying updates is a major headache
- having to learn a new way of doing things for questionable benefits

I'm told the benefits are:
- easier to design/edit/manage the front-end
- easier (automatic?) to have the site be responsive
- some built-in functionality that we might use, for accounts, comments, searching, etc?

I don't personally see the benefits of using a Content Management System for this kind of project, where managing the content is a very small aspect of the bigger picture. Using the CMS as a base for what is otherwise a custom-coded project, and having to adapt to fit the CMS's architecture. It seems any benefits would be outweighed by the downsides. Am I wrong here?